NAME

Bio::Tools::Glimmer - parser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions

SYNOPSIS

   use Bio::Tools::Glimmer;

   # file
   my $parser = Bio::Tools::Glimmer->new(-file => $file);
   # filehandle:
   $parser = Bio::Tools::Glimmer->new( -fh  => \*INPUT );
   # provide a sequence identifier (Glimmer 2.X)
   my $parser = Bio::Tools::Glimmer->new(-file => $file, -seqname => seqname);
   # force format (override automatic detection)
   my $parser = Bio::Tools::Glimmer->new(-file => $file, -format => 'GlimmerM');

   # parse the results
   # note: this class is-a Bio::Tools::AnalysisResult which implements
   # Bio::SeqAnalysisParserI, i.e., $glimmer->next_feature() is the same

   while(my $gene = $parser->next_prediction()) {
       # For eukaryotic input (GlimmerM/GlimmerHMM), $gene will be an instance
       # of Bio::Tools::Prediction::Gene, which inherits off
       # Bio::SeqFeature::Gene::Transcript, and $gene->exons() will return an
       # array of Bio::Tools::Prediction::Exon objects.
       # For prokaryotic input (Glimmer2.X/Glimmer3.X), $gene will be an
       # instance of Bio::SeqFeature::Generic

       # all exons (eukaryotic only):
       @exon_arr = $gene->exons();
       # initial exons only
       @init_exons = $gene->exons('Initial');
       # internal exons only
       @intrl_exons = $gene->exons('Internal');
       # terminal exons only
       @term_exons = $gene->exons('Terminal');
   }

DESCRIPTION

This is a module for parsing Glimmer, GlimmerM and GlimmerHMM predictions. It will create gene objects from the prediction report which can be attached to a sequence using Bioperl objects, or output as GFF suitable for loading into Bio::DB::GFF for use with Gbrowse.

Glimmer is open source and available at <http://www.cbcb.umd.edu/software/glimmer/>.

GlimmerM is open source and available at <http://www.tigr.org/software/glimmerm/>.

GlimmerHMM is open source and available at <http://www.cbcb.umd.edu/software/GlimmerHMM/>.

Note that Glimmer 2.X will only process the first sequence in a fasta file, and the prediction report does not contain any sort of sequence identifier

Note that Glimmer 3.X produces two output files. This module only parses the .predict file.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

bioperl-l@bioperl.org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via email or the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Torsten Seemann

Mark Johnson

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::Tools::Glimmer->new();
 Function: Builds a new Bio::Tools::Glimmer object 
 Returns : an instance of Bio::Tools::Glimmer
 Args    : format ('Glimmer', 'GlimmerM', 'GlimmerHMM'), seqname

analysis_method

 Usage     : $glimmer->analysis_method();
 Purpose   : Inherited method. Overridden to ensure that the name matches
             /glimmer/i.
 Returns   : String
 Argument  : n/a

next_feature

 Title   : next_feature
 Usage   : while($gene = $glimmer->next_feature()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Glimmer result
           file. Call this method repeatedly until FALSE is returned.

           The returned object is actually a SeqFeatureI implementing object.
           This method is required for classes implementing the
           SeqAnalysisParserI interface, and is merely an alias for 
           next_prediction() at present.

 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

next_prediction

 Title   : next_prediction
 Usage   : while($gene = $glimmer->next_prediction()) {
                  # do something
           }
 Function: Returns the next gene structure prediction of the Glimmer result
           file. Call this method repeatedly until FALSE is returned.

 Example :
 Returns : A Bio::Tools::Prediction::Gene object.
 Args    :

_parse_predictions

 Title   : _parse_predictions()
 Usage   : $obj->_parse_predictions()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns :

_parse_eukaryotic

 Title   : _parse_eukaryotic()
 Usage   : $obj->_parse_eukaryotic()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns :

_parse_prokaryotic

 Title   : _parse_prokaryotic()
 Usage   : $obj->_parse_prokaryotic()
 Function: Parses the prediction section. Automatically called by
           next_prediction() if not yet done.
 Example :
 Returns :

_prediction

 Title   : _prediction()
 Usage   : $gene = $obj->_prediction()
 Function: internal
 Example :
 Returns :

_add_prediction

 Title   : _add_prediction()
 Usage   : $obj->_add_prediction($gene)
 Function: internal
 Example :
 Returns :

_predictions_parsed

 Title   : _predictions_parsed
 Usage   : $obj->_predictions_parsed
 Function: internal
 Example :
 Returns : TRUE or FALSE

_seqname

 Title   : _seqname
 Usage   : $obj->_seqname($seqname)
 Function: internal (for Glimmer 2.X)
 Example :
 Returns : String

_seqlength

 Title   : _seqlength
 Usage   : $obj->_seqlength($seqlength)
 Function: internal (for Glimmer 2.X)
 Example :
 Returns : String

_format

 Title   : _format
 Usage   : $obj->_format($format)
 Function: internal
 Example :
 Returns : String

_detail_file

 Title   : _detail_file
 Usage   : $obj->_detail_file($filename)
 Function: internal (for Glimmer 3.X)
 Example :
 Returns : String